So this used to work verbatim. the second ampersand is b/c the python script never returns so i would like to Omega LED to stop flashing and finish the boot sequence. Also, the device is used as an AVR Programmer using AVR dude (from the arduino dock 2 package with a modified avrdude config file), so the device shouldn't be powered on longer than a single day. I could possibly remove the ampersand from the setup line.
I removed the setup shell and replaced it with the gpiomux commands directly and that seem to correct my issues
also the python pyGPIO module has a bug in it that I can't spend time trying to address ATM. So i just worked around it.